Family pairwise search with embedded motif models.

MOTIVATION: Statistical models of protein families, such as position-specific scoring matrices, profiles and hidden Markov models, have been used effectively to find remote homologs when given a set of known protein family members. Unfortunately, training these models typically requires a relatively large set of training sequences. Recent work (Grundy, J. Comput. Biol., 5,<479-492, 1998) has shown that, when only a few family members are known, several theoretically justified statistical modeling techniques fail to provide homology detection performance on a par with Family Pairwise Search (FPS), an algorithm that combines scores from a pairwise sequence similarity algorithm such as BLAST. RESULTS: The present paper provides a model-based algorithm that improves FPS by incorporating hybrid motif-based models of the form generated by Cobbler (Henikoff and Henikoff, Protein Sci., 6, 698-705, 1997). For the 73 protein families investigated here, this cobbled FPS algorithm provides better homology detection performance than either Cobbler or FPS alone. This improvement is maintained when BLAST is replaced with the full Smith-Waterman algorithm. AVAILABILITY: http://fps.sdsc.edu     

Flux Analysis of Glucose Metabolism in Rhizopus oryzae for the Purpose of Increasing Lactate Yields

A flux analysis of glucose metabolism in the filamentous fungus Rhizopus oryzae was achieved using a specific radioactivity curve-matching program, TFLUX. Glycolytic and tricarboxylic acid cycle intermediates labeled through the addition of extracellular [U-14C]glucose were isolated and purified for specific radioactivity determinations. This information, together with pool sizes and the rates of glucose utilization and end product production, provided input for flux maps of the metabolic network under two different experimental conditions. Based upon the flux analysis of this system, a mutant of R. oryzae with higher lactate and lower ethanol yields than the parent was sought for and found.     

A Mass-Rearing Method for the Assassin Bug Pristhesancus plagipennis (Hemiptera: Reduviidae)

Pristhesancus plagipennis (Walker) is a predator of larvae and nymphs of many pestiferous insects for which natural enemies are not commercially available. This paper describes a containerized mass-rearing method for P. plagipennis using hot water-killed larvae of Tenebrio molitor (L.) and Helicoverpa armigera (Hübner). In addition, the effect of P. plagipennis density during nymphal rearing and adult oviposition was investigated. The rearing method minimizes P. plagipennis cannibalism, avoids the need for live insect prey, and is space and labor efficient. Larvae of the yellow mealworm, T. molitor, were the most suitable prey for minimizing nymphal development time and mortality while producing insects with the highest body weight. When reared on a diet of T. molitor, the optimum rearing density was 20–27 nymphs per 5-liter container. This rearing density minimized nymphal mortality to 16–22%. The optimum density for oviposition was 16 adults per 5-liter container, which provided the best compromise between egg production and space utilization.     

Augmentation of the assassin bug Pristhesancus plagipennis (Walker) (Hemiptera: Reduviidae) as a biological control agent for Helicoverpa spp. in cotton

Third-instar nymphs of the Australian assassin bug, Pristhesancus plagipennis (Walker), were released into cotton plots at two release densities and two crop growth stages to test their biological control potential. Release rates of 2 and 5 nymphs per metre row resulted in field populations of 0.51 and 1.38 nymphs per metre row, respectively, indicating that over 70% of nymphs died or emigrated within two weeks of release. Effective release rates of 1.38 nymphs per metre row reduced the number of Helicoverpa spp. larvae in the plots for a 7-week period. Crop yields were significantly greater in the plots to which P. plagipennis nymphs were released, with the effective release rate of 1.38 nymphs per metre row providing equivalent yields as insecticide treated plots. The data suggest that P. plagipennis has the capacity to reduce Helicoverpa spp. larvae densities in cotton crops when augmented through inundative release.     

TP53 Mutational Status Is a Potential Marker for Risk Stratification in Wilms Tumour with Diffuse Anaplasia

Purpose

The presence of diffuse anaplasia in Wilms tumours (DAWT) is associated with TP53 mutations and poor outcome. As patients receive intensified treatment, we sought to identify whether TP53 mutational status confers additional prognostic information.

Patients and Methods

We studied 40 patients with DAWT with anaplasia in the tissue from which DNA was extracted and analysed for TP53 mutations and 17p loss. The majority of cases were profiled by copy number (n = 32) and gene expression (n = 36) arrays. TP53 mutational status was correlated with patient event-free and overall survival, genomic copy number instability and gene expression profiling.

Results

From the 40 cases, 22 (55%) had TP53 mutations (2 detected only after deep-sequencing), 20 of which also had 17p loss (91%); 18 (45%) cases had no detectable mutation but three had 17p loss. Tumours with TP53 mutations and/or 17p loss (n = 25) had an increased risk of recurrence as a first event (p = 0.03, hazard ratio (HR), 3.89; 95% confidence interval (CI), 1.26–16.0) and death (p = 0.04, HR, 4.95; 95% CI, 1.36–31.7) compared to tumours lacking TP53 abnormalities. DAWT carrying TP53 mutations showed increased copy number alterations compared to those with wild-type, suggesting a more unstable genome (p = 0.03). These tumours showed deregulation of genes associated with cell cycle and DNA repair biological processes.

Conclusion

This study provides evidence that TP53 mutational analysis improves risk stratification in DAWT. This requires validation in an independent cohort before clinical use as a biomarker.     

Influence of mevinolin on metabolism of low density lipoproteins in primary moderate hypercholesterolemia

Mevinolin, a competitive inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A reductase, was used for treatment of 12 patients with moderate hypercholesterolemia, but not classical familial hypercholesterolemia. For most patients, measurements of turnover of low density lipoprotein-apolipoprotein B (LDL-apoB) were made on placebo and during treatment with two doses of mevinolin. LDL turnover was determined after injection of autologous 125I-labeled radioiodinated LDL. Compared to placebo, a low dose of mevinolin (10 mg, twice daily (BID] caused reductions of plasma total cholesterol and LDL-cholesterol averaging 15% and 20%, respectively; corresponding reductions on high doses of mevinolin (20 mg BID) were 22% and 31%, respectively. Triglyceride levels were unchanged by the drug. High density lipoprotein cholesterol levels rose significantly on the high dose, but not on the low dose. Neither dose produced a stastistically significant change in fractional catabolic rate (FCR) for LDL-apoB for the whole group, although several patients had increases in FCR on both doses. In contrast, both doses of mevinolin caused decreases in production rates of LDL-apoB. Thus, the fall in LDL levels in patients with moderate hypercholesterolemia can be explained more by a reduction in the input rate of LDL-apoB than by enhanced fractional removal of LDL from the circulation.     

Studies on the metabolism of apolipoprotein B in hypertriglyceridemic subjects using simultaneous administration of tritiated leucine and radioiodinated very low density lipoprotein

To study the metabolic pathways of apolipoprotein B (apoB), a series of studies were carried out in which both radioiodinated very low density lipoproteins (VLDL) and tritiated leucine were simultaneously injected into three hypertriglyceridemic subjects. The appearance and disappearance of tritium activity in VLDL apoB, intermediate density lipoprotein (IDL) apoB, and low density lipoprotein (LDL) apoB were followed as was the disappearance of iodine activity from VLDL and the appearance and disappearance of iodine activity in IDL apoB and LDL apoB. It was found that a delipidation chain could describe the kinetics of both endogenously and exogenously labeled VLDL. A slow component of VLDL was necessary to fit the VLDL 131I-labeled apoB data and was consistent with the observed VLDL [3H]apoB kinetics. In addition, the estimated rate of conversion of VLDL apoB to LDL exceeded that which appeared to pass through the measured IDL pools, suggesting that a fraction of the IDL was not directly observed. It was also found that a higher percentage of VLDL 131I-labeled apoB was converted to LDL apoB than was VLDL [3H]apoB. To evaluate possible causes of this apparent anomaly, simultaneous examination of all kinetic data was performed. This exercise resulted in the resolution of removal pathways from multiple compartments in the VLDL delipidation chain and the conversion of slowly metabolized VLDL to IDL and LDL. The wide spectrum of this loss pathway indicates that previous estimates of VLDL apoB production rate using the radioiodinated methodology probably represent lower bounds for the true physiologic variable. It is important to note that these direct losses were apparent only when the combination of endogenous and exogenous labeling was used.